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The number of people, including recreational athletes, taking part in long running or cycling events is increasing. Research has shown that as many as 30–90% of athletes have experienced at least one of the gastrointestinal symptoms. The frequency of symptoms increases heavily with a workout intensity over 70% of maximal oxygen consumption and is lesser with recreational sport activities. The most frequent gastrointestinal symptoms are gastroesophageal reflux, belching, abdominal cramping and pain, urge to defecate, flatulence, diarrhoea, and intestinal bleeding. The most important cause of the symptoms is reduced blood flow through splanchnic vessels because of the blood shift towards the muscles, leading to intestinal ischemia. Intestinal ischemia is a physiological response of the organism to strenuous exercise and cannot be prevented. If it is long-lasting, it leads to damage of the intestinal wall, increased permeability of intestinal mucosa with consequential endotoxemia, inflammation, reduced protection from gastric acid and digestive enzymes, ulcers and in extreme cases ischemic necrosis. Contributing factors to the damage of intestines and its symptoms are also mechanical causes, dehydration, inappropriate diet and certain drugs, especially non-steroid antiinflammatory drugs. Even though we cannot completely prevent the development of injuries and symptoms, we can to a certain degree reduce the risk with gradual adjustment of intestines to consuming food and drinks during prolonged sports activity, good hydration, appropriate diet based on reducing the intake of certain substances that do not resorb well (such as lactose, fructose, fiber), adequate intake of easily digestible carbohydrates, and with intake of proton pump inhibitors directly before sports activity. Possible positive effects of fats, substances that affect the production of vasodilatative mediator nitric oxide (glutamine, arginine, citruline, nitrates and nitrites) and probiotics, are also being studied.